Edwards-Venn-diagrams.R

rm(list = ls())
#BiocManager::install(c("RBGL","graph"))
#install.packages("Vennerable", repos="http://R-Forge.R-project.org")
library(Vennerable)

## Loading required package: graph

## Loading required package: BiocGenerics

## Loading required package: parallel

## 
## Attaching package: 'BiocGenerics'

## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB

## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs

## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
##     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
##     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
##     union, unique, unsplit, which, which.max, which.min

## Loading required package: RBGL

## Loading required package: grid

## Loading required package: lattice

## Loading required package: RColorBrewer

## Loading required package: reshape

## Warning: package 'reshape' was built under R version 4.0.3

## Loading required package: gtools

## Loading required package: xtable

data(StemCell)
class(StemCell)

## [1] "list"

#View(StemCell)
names(StemCell)

## [1] "OCT4"  "SOX2"  "NANOG" "E2F4"

StemCell[[1]][1:10]

##  [1] "AASDH"    "ABTB2"    "ACCN4"    "ACD"      "ADAMTS16" "ADAMTSL1"
##  [7] "ADD3"     "ADRA1A"   "ADRA2A"   "ALKBH"

VennRaw <- Venn(StemCell)
VennRaw

## A Venn object on 4 sets named
## OCT4,SOX2,NANOG,E2F4 
## 0000 1000 0100 1100 0010 1010 0110 1110 0001 1001 0101 1101 0011 1011 0111 1111 
##    0  109  305   45  644   64  354  287  821   30   78    6  118   16  138   66

Venn3 <- VennRaw[, c("OCT4", "SOX2", "NANOG")]
Venn3 

## A Venn object on 3 sets named
## OCT4,SOX2,NANOG 
## 000 100 010 110 001 101 011 111 
## 821 139 383  51 762  80 492 353

########circles", "squares", "triangles", or "AWFE"
plot(Venn3, doWeights = T)

plot(Venn3, doWeights = F)

plot(VennRaw, doWeights = F,type="AWFE")

plot(VennRaw, doWeights = T,type="AWFE")

plot(Venn3,type="squares")

plot(Venn3,type="triangles")

??Vennerable

## starting httpd help server ...

##  done

#https://harrycaufield.net/severalog/2015/5/7/venn-diagrams-in-r-or-how-to-go-around-in-circles
#help(Vennerable)